GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00870 in Sinorhizobium meliloti 1021

Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate SMc00078 SMc00078 Leu/Ile/Val-binding protein

Query= uniprot:D8IUY1
         (378 letters)



>FitnessBrowser__Smeli:SMc00078
          Length = 368

 Score =  182 bits (461), Expect = 2e-50
 Identities = 125/376 (33%), Positives = 194/376 (51%), Gaps = 21/376 (5%)

Query: 4   RVSGLNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQ 63
           R++G+  +AAS+A  P  A A  T    IG  +PLTGP A+ G+  + G   A+E +N+ 
Sbjct: 5   RLTGM-ALAASVAFAP-LAHADIT----IGVITPLTGPVAAFGEQVKNGAEAAVEAINSA 58

Query: 64  PITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAG 123
              V G+K+   ++  DD  +PK  V+VA +LA +G++ +VGP  SG ++PAS V  + G
Sbjct: 59  G-GVNGEKLVVKIV--DDAGEPKQAVSVANQLAGEGIQYVVGPVLSGTSMPASDVLAENG 115

Query: 124 IVVAT-VASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQG 182
           I++ T  A+ P +T +G   + R    D Q     A Y  K  K KRVAV+ D+ AYG+G
Sbjct: 116 ILMVTPTATTPDLTTRGLWNVLRTCGRDDQQAVVAADYVVKNFKDKRVAVLHDKGAYGKG 175

Query: 183 LAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQM 242
           LA  F     A GI  V  +       DF AI+T +K +  D V+ GGY  +GG + RQM
Sbjct: 176 LADGFKAAINAGGITEVVYEGLTPGEKDFGAIVTRLKAENVDVVYFGGYHAEGGLLARQM 235

Query: 243 KQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNR 302
              GV   L+GGDG+ + E   +GG+A   +VY        + A    +   E  K  N 
Sbjct: 236 HDQGVKAQLLGGDGLSNTEFWAIGGEAASGTVYTNASDATRNPAAAPVI---EALKAKNI 292

Query: 303 PAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKG-----VAGQYDFDANHDL 357
           PAE + ++ Y  + ++   +++A S +      A+A     G     V G+  +  + DL
Sbjct: 293 PAEAFTLNAYAAVQVLKAGIEKAGSTED---ATAVATAIKSGEAIDTVIGKLTYGESGDL 349

Query: 358 KQSPVTVYRFKDGLPV 373
                ++Y+++ G  V
Sbjct: 350 TSPSFSLYKWEGGQSV 365


Lambda     K      H
   0.316    0.134    0.378 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 417
Number of extensions: 18
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 378
Length of database: 368
Length adjustment: 30
Effective length of query: 348
Effective length of database: 338
Effective search space:   117624
Effective search space used:   117624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory